# Coordinate Gene Regulation in Animal Cells

> **NIH NIH R01** · CORNELL UNIVERSITY · 2020 · $466,287

## Abstract

Summary/Abstract:
The genomes of higher organisms are highly regulated and their expression can respond to a variety of
developmental, environmental, and nutritional cues. The failure to execute proper gene regulation can lead to
developmental defects and disease states. A broad goal of this research is to understand basic regulatory
mechanisms of genes at the level of transcription, the stage where RNA polymerase II (Pol II) transcribes the
genes into mRNA. Studies of Drosophila heat shock (HS) genes, and more recently mammalian genes, have
revealed that regulation by transcription factors (TFs) in vivo can occur at a point after Pol II has initiated
transcription and has elongated to sites 20 to 60 bases downstream where it pauses. This proximal-promoter
pausing in early transcriptional elongation is a rate-limiting and often regulated step in transcription. In contrast,
traditional models of transcription regulation, based mainly in studies of microbes, indicated that transcription
regulation occurs primarily at the recruitment of Pol II to promoters. Understanding the regulatory contributions
and molecular mechanisms of TFs at three critical steps; 1) Pol II recruitment, 2) promoter-proximal pausing,
and 3) the regulated release from the paused Pol II to productive elongation, are foci of this renewal. A battery
of complementary approaches (some novel) are designed to disrupt (as rapidly as possible) critical TFs
involved in transcription regulation, while high spatial and temporal resolution assays will allow Pol II and TFs
to be observed across the genome both before and during a time-course of gene activation. These
observational assays include highly-sensitive PRO-seq assay for mapping the position and amount of engaged
Pol II across genes and genomes, and ChIP-nexus for mapping the position of specific transcription factors
genome-wide. Both provide near base-pair resolution, which is critical in evaluating regulatory mechanisms.
We will use three experimental systems Drosophila; mammalian cell lines, and S. pombe, and each has a
foundation of available tools and existing data sets that can be uniquely exploited. Together, these systems will
assess the generalities of our regulatory models. They are designed to reveal in many cases the primary
effects of disruption of particular TFs, catalytic activity and macromolecular interaction domains. Aim 1 tests
the mechanistic role of TFs, like GAGA factor and M1BP, and the NURF remodeler, in recruitment of Pol II to
promoters and enhancers, and test candidate mammalian factors for comparable roles. Aim 2 tests the
mechanistic role of pausing factors NELF and DSIF, and general transcription factors in stabilizing Pol II
pausing at both promoters and enhancers. Aim 3 tests the role of TFs in the release of Pol II to productive
elongation. While Aims 1-3 seek to disrupt a TF, Aim 4 directly recruits TF domains and coactivators to
explore their roles, again using genome-wide high-resolution assays....

## Key facts

- **NIH application ID:** 9901535
- **Project number:** 5R01GM025232-43
- **Recipient organization:** CORNELL UNIVERSITY
- **Principal Investigator:** JOHN T LIS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $466,287
- **Award type:** 5
- **Project period:** 1978-04-01 → 2021-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9901535

## Citation

> US National Institutes of Health, RePORTER application 9901535, Coordinate Gene Regulation in Animal Cells (5R01GM025232-43). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9901535. Licensed CC0.

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